fitThresh

This function uses the discrete approximation of Boucher and Demery (2016) to fit a multi-state discrete character threshold model following Felsenstein (2012; Revell 2014).

phylogenetics

comparative method

discrete character

ancestral states

A wide range of methods for phylogenetic analysis - concentrated in phylogenetic comparative biology, but also including numerous techniques for visualizing, analyzing, manipulating, reading or writing, and even inferring phylogenetic trees. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, and simulation of phylogenies and trait data. A broad range of plotting methods for phylogenies and comparative data include (but are not restricted to) methods for mapping trait evolution on trees, for projecting trees into phenotype space or a onto a geographic map, and for visualizing correlated speciation between trees. Lastly, numerous functions are designed for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data. For instance, there are functions for computing consensus phylogenies from a set, for simulating phylogenetic trees and data under a range of models, for randomly or non-randomly attaching species or clades to a tree, as well as for a wide range of other manipulations and analyses that phylogenetic biologists might find useful in their research.

Liam Revell

phytools

Phylogenetic Tools for Comparative Biology (and Other Things)

fitThresh function

<dl>	<dt>tree</dt>
<dd>object of class <code>"phylo"</code>.</dd>	<dt>x</dt>
<dd>a named vector.</dd>	<dt>sequence</dt>
<dd>assumed ordering of the discrete character state. If not supplied and then alphanumeric order is assumed.</dd>	<dt>...</dt>
<dd>optional arguments.</dd></dl>

Arguments

Liam Revell <a href="/link/liam.revell%40umb.edu?package=phytools&version=2.3-0" data-mini-rdoc="phytools::liam.revell@umb.edu">liam.revell@umb.edu</a>

Author

Fits multi-state threshold model using the discrete approximation — fitThresh

<dl>

	<dt>tree</dt>
<dd>object of class <code>"phylo"</code>.</dd>

	<dt>x</dt>
<dd>a named vector.</dd>

	<dt>sequence</dt>
<dd>assumed ordering of the discrete character state. If not supplied and then alphanumeric order is assumed.</dd>

	<dt>...</dt>
<dd>optional arguments.</dd>

</dl>

Liam Revell <a href='mailto:liam.revell@umb.edu'>liam.revell@umb.edu</a>

fitThresh: Fits multi-state threshold model using the discrete approximation

Description

Usage

Value

Arguments

Author

References

See Also